Given that there are about 10- to 100-thousand genes and most mutations result in subtle phenotypes, a mutational analysis of all genes individually would be highly inefficient. Therefore, we have developed a method for systematically scanning the genome for interesting phenotypes by introducing deletions spanning up to a Megabase of chromosomal DNA. This "deletion scanning" employs the Cre/lox system of site-specific recombination in murine embryonic stem cells and allows to systematically scan along a chromosome for mutations with interesting phenotypes. We have worked out and built the vector cassettes to receive the different genomic fragments spaced along a chromosome. We have worked out the conditions for co-transfection of Cre-recombinase with these vectors. We are now starting to proceed along mouse chromosome 16 with a systematic in vivo mutational analysis.